Load Data from the Clock Calculator

## We have 132 observations with 102 columns.

Duplicated Observations

We have 3 subjects (SIDs: CQ 1328, CQ 1424, CQ 1518) with duplicated observations.

Clocks stable?

In section, we check if the clocks are stable by comparing them in the duplicated observations.

Concordance between pairs

Evaluate correlation/concordance between the duplicate pairs

Absolute differences in two observations

Clocks / Age Accelerations

##      Horvath EAA Hannum EAA PhenoAge EAA Skin&Blood EAA GrimAge EAA     DNAmTL
## [1,]  0.05638483   2.678389     3.898440      0.6858806   0.7138976 0.04309056
## [2,]  2.80993321   1.122348     2.464987      0.8001586   1.6632470 0.04052281
## [3,]  1.23251949   0.732867     7.594791      2.9191094   1.0295776 0.02069328
##           IEAA     EEAA
## [1,] 0.3889968 3.667739
## [2,] 3.3026780 1.740232
## [3,] 0.9771748 3.076599
## 
## Summary: :
##      Horvath EAA Hannum EAA PhenoAge EAA Skin&Blood EAA GrimAge EAA     DNAmTL
## mean    1.366279   1.511201     4.652739       1.468383   1.1355741 0.03476888
## sd      1.381639   1.029403     2.646780       1.257665   0.4834692 0.01225725
##          IEAA      EEAA
## mean 1.556283 2.8281897
## sd   1.540750 0.9874722

ICC of each clock

## 
##  Horvath EAA : 
##                          type       ICC        F df1 df2           p
## Single_raters_absolute   ICC1 0.9802908 100.4755   2   3 0.001783993
## Single_random_raters     ICC2 0.9803666 165.2373   2   2 0.006015498
## Single_fixed_raters      ICC3 0.9879690 165.2373   2   2 0.006015498
## Average_raters_absolute ICC1k 0.9900473 100.4755   2   3 0.001783993
## Average_random_raters   ICC2k 0.9900860 165.2373   2   2 0.006015498
## Average_fixed_raters    ICC3k 0.9939481 165.2373   2   2 0.006015498
## 
##  Hannum EAA : 
##                          type       ICC        F df1 df2          p
## Single_raters_absolute   ICC1 0.9241935 25.38296   2   3 0.01318018
## Single_random_raters     ICC2 0.9242641 26.02300   2   2 0.03700552
## Single_fixed_raters      ICC3 0.9259890 26.02300   2   2 0.03700552
## Average_raters_absolute ICC1k 0.9606035 25.38296   2   3 0.01318018
## Average_random_raters   ICC2k 0.9606416 26.02300   2   2 0.03700552
## Average_fixed_raters    ICC3k 0.9615725 26.02300   2   2 0.03700552
## 
##  PhenoAge EAA : 
##                          type       ICC        F df1 df2         p
## Single_raters_absolute   ICC1 0.3206087 1.943812   2   3 0.2874602
## Single_random_raters     ICC2 0.3206087 1.943812   2   2 0.3396956
## Single_fixed_raters      ICC3 0.3206087 1.943812   2   2 0.3396956
## Average_raters_absolute ICC1k 0.4855469 1.943812   2   3 0.2874602
## Average_random_raters   ICC2k 0.4855469 1.943812   2   2 0.3396956
## Average_fixed_raters    ICC3k 0.4855469 1.943812   2   2 0.3396956
## 
##  Skin&Blood EAA : 
##                          type       ICC       F df1 df2         p
## Single_raters_absolute   ICC1 0.3135357 1.91348   2   3 0.2913003
## Single_random_raters     ICC2 0.3135357 1.91348   2   2 0.3432322
## Single_fixed_raters      ICC3 0.3135357 1.91348   2   2 0.3432322
## Average_raters_absolute ICC1k 0.4773919 1.91348   2   3 0.2913003
## Average_random_raters   ICC2k 0.4773919 1.91348   2   2 0.3432322
## Average_fixed_raters    ICC3k 0.4773919 1.91348   2   2 0.3432322
## 
##  GrimAge EAA : 
##                          type       ICC        F df1 df2           p
## Single_raters_absolute   ICC1 0.9807695 103.0017   2   3 0.001719697
## Single_random_raters     ICC2 0.9809233 636.9022   2   2 0.001567638
## Single_fixed_raters      ICC3 0.9968647 636.9022   2   2 0.001567638
## Average_raters_absolute ICC1k 0.9902914 103.0017   2   3 0.001719697
## Average_random_raters   ICC2k 0.9903698 636.9022   2   2 0.001567638
## Average_fixed_raters    ICC3k 0.9984299 636.9022   2   2 0.001567638
## 
##  DNAmTL : 
##                          type       ICC        F df1 df2           p
## Single_raters_absolute   ICC1 0.9898538 196.1186   2   3 0.000661295
## Single_random_raters     ICC2 0.9898538 196.1186   2   2 0.005073088
## Single_fixed_raters      ICC3 0.9898538 196.1186   2   2 0.005073088
## Average_raters_absolute ICC1k 0.9949010 196.1186   2   3 0.000661295
## Average_random_raters   ICC2k 0.9949010 196.1186   2   2 0.005073088
## Average_fixed_raters    ICC3k 0.9949010 196.1186   2   2 0.005073088
## 
##  IEAA : 
##                          type       ICC        F df1 df2           p
## Single_raters_absolute   ICC1 0.9750351 79.11262   2   3 0.002538238
## Single_random_raters     ICC2 0.9750756 90.94104   2   2 0.010876536
## Single_fixed_raters      ICC3 0.9782469 90.94104   2   2 0.010876536
## Average_raters_absolute ICC1k 0.9873598 79.11262   2   3 0.002538238
## Average_random_raters   ICC2k 0.9873805 90.94104   2   2 0.010876536
## Average_fixed_raters    ICC3k 0.9890039 90.94104   2   2 0.010876536
## 
##  EEAA : 
##                          type       ICC        F df1 df2          p
## Single_raters_absolute   ICC1 0.8698274 14.36421   2   3 0.02907429
## Single_random_raters     ICC2 0.8698274 14.36421   2   2 0.06508632
## Single_fixed_raters      ICC3 0.8698274 14.36421   2   2 0.06508632
## Average_raters_absolute ICC1k 0.9303825 14.36421   2   3 0.02907429
## Average_random_raters   ICC2k 0.9303825 14.36421   2   2 0.06508632
## Average_fixed_raters    ICC3k 0.9303825 14.36421   2   2 0.06508632

Remove duplicated observations

Number of observations removed: 3

Missing values

For each exposure measurements:

Number of missing values in baseline covariates:

##             Age             BMI predictedGender        fueltype       stovetype 
##               0               0               0               0               0

Number of missing values in ambient exposure measurements covariates:

##  bap_air pm25_air  ANY_air  BPE_air  BaA_air  BbF_air  BkF_air  CHR_air 
##        5        0       41        5        5        5        5        5 
##  DBA_air  FLT_air  FLU_air  IPY_air  NAP_air  PHE_air  PYR_air 
##        5        5       41        5       41       41        5

Number of missing values in urinary measurements covariates:

## Benzanthracene_Chrysene_urine             Naphthalene_urine 
##                             2                             0 
##     Methylnaphthalene_2_urine     Methylnaphthalene_1_urine 
##                             9                             4 
##            Acenaphthene_urine Phenanthrene_Anthracene_urine 
##                             0                             0 
##            Fluoranthene_urine                  Pyrene_urine 
##                             0                            18

For each observations:

Observations with different number of total missing measurements:

##                                                       
## Number of missing measurements:  0  1 2 3  4 5 6 14 15
## Number of observations:         73 10 4 1 27 8 1  3  2

Observations with different number of missing air exposure measurements:

##                                         
## Number of missing measurements:  0  4 14
## Number of observations:         88 36  5

Observations with different number of missing urinary measurements:

##                                           
## Number of missing measurements:   0  1 2 3
## Number of observations:         103 20 5 1

Number of observations removed: 0

Table with summarize info [table 1]

Characteristic N = 1291
Age 58 (15)
BMI 22.0 (3.5)
predictedGender
female 129 / 129 (100%)
fueltype
Plant 4 / 129 (3.1%)
Smokeles 18 / 129 (14%)
Smoky 98 / 129 (76%)
Wood 9 / 129 (7.0%)
stovetype
FP 11 / 129 (8.5%)
HS 31 / 129 (24%)
LS 30 / 129 (23%)
Mix 37 / 129 (29%)
PS 20 / 129 (16%)
DNAmAge 59 (13)
DNAmAgeHannum 60 (14)
DNAmPhenoAge 56 (14)
DNAmAgeSkinBloodClock 57 (13)
DNAmGrimAge 56 (11)
DNAmTL 6.82 (0.32)
AgeAccelerationResidual -0.1 (4.4)
AgeAccelerationResidualHannum -0.1 (4.0)
AgeAccelPheno 0.0 (4.3)
DNAmAgeSkinBloodClockAdjAge 0.0 (3.4)
AgeAccelGrim -0.09 (2.99)
DNAmTLAdjAge 0.00 (0.18)
IEAA 0.0 (4.1)
EEAA -0.1 (5.1)
bap_air 65 (87)
(Missing) 5
pm25_air 197 (176)
ANY_air 1,038 (1,792)
(Missing) 41
BPE_air 71 (92)
(Missing) 5
BaA_air 88 (145)
(Missing) 5
BbF_air 106 (143)
(Missing) 5
BkF_air 23 (32)
(Missing) 5
CHR_air 83 (133)
(Missing) 5
DBA_air 24 (36)
(Missing) 5
FLT_air 60 (136)
(Missing) 5
FLU_air 486 (680)
(Missing) 41
IPY_air 43 (51)
(Missing) 5
NAP_air 5,731 (8,737)
(Missing) 41
PHE_air 730 (1,054)
(Missing) 41
PYR_air 66 (139)
(Missing) 5
Benzanthracene_Chrysene_urine 0.92 (3.17)
(Missing) 2
Naphthalene_urine 224 (686)
Methylnaphthalene_2_urine 46 (59)
(Missing) 9
Methylnaphthalene_1_urine 20 (24)
(Missing) 4
Acenaphthene_urine 7 (11)
Phenanthrene_Anthracene_urine 204 (275)
Fluoranthene_urine 21 (23)
Pyrene_urine 0.71 (0.57)
(Missing) 18

1 Mean (SD); n / N (%)

PCA

Explore clocks

Correlogram

Between clocks

Median absolute error

##               DNAmAge         DNAmAgeHannum          DNAmPhenoAge 
##              3.391653              3.380488              3.005900 
## DNAmAgeSkinBloodClock           DNAmGrimAge 
##              2.585191              4.063720

Scatterplots of age vs each epigenetic age

Explore Exposure Measurements

Correlogram

Between Ambient Exposure Measurements

Between Urinary Exposure Measurements

Between Ambient and Urinary Exposure Measurements

Clocks vs Measurements

Pairplots

New data of fuelExp

Childhood Exposure

All subjects

Characteristic N = 2241
brthFuel
Mix 101 / 220 (46%)
Smokeles 9 / 220 (4.1%)
Smoky 78 / 220 (35%)
Wood 32 / 220 (15%)
(Missing) 4

1 n / N (%)

subjects with DNA methylation data

Characteristic N = 1291
brthFuel
Mix 54 / 126 (43%)
Smokeles 7 / 126 (5.6%)
Smoky 52 / 126 (41%)
Wood 13 / 126 (10%)
(Missing) 3

1 n / N (%)

Lifetime Exposure

All subjects

Characteristic N = 2241
cumFuel
Mix 168 / 224 (75%)
Smoky 56 / 224 (25%)

1 n / N (%)

subjects with DNA methylation data

Characteristic N = 1291
cumFuel
Mix 87 / 129 (67%)
Smoky 42 / 129 (33%)

1 n / N (%)

Fueltype from our original dataset

All subjects

Characteristic N = 2241
fueltype
Plant 4 / 129 (3.1%)
Smokeles 18 / 129 (14%)
Smoky 98 / 129 (76%)
Wood 9 / 129 (7.0%)
(Missing) 95

1 n / N (%)

subjects with DNA methylation data

Characteristic N = 2241
fueltype
Plant 4 / 129 (3.1%)
Smokeles 18 / 129 (14%)
Smoky 98 / 129 (76%)
Wood 9 / 129 (7.0%)
(Missing) 95

1 n / N (%)

Control Subjects

## # A tibble: 6 × 14
##   ids_LCW VISIT education_cat SbjctD_LEX loc_N loc_E grp            dist_min
##   <chr>   <lgl>         <dbl> <lgl>      <dbl> <dbl> <chr>             <dbl>
## 1 1824    NA                3 NA          26.2  104. LCW Clean Ctrl    0.347
## 2 1912    NA                5 NA          26.2  104. LCW Clean Ctrl    0.347
## 3 2276    NA                6 NA          26.2  104. LCW Clean Ctrl    0.347
## 4 4386    NA                2 NA          25.7  104. LCW Clean Ctrl    0.570
## 5 2394    NA                2 NA          26.2  104. LCW Clean Ctrl    0.607
## 6 2274    NA                5 NA          26.2  104. LCW Clean Ctrl    0.609
## # … with 6 more variables: inpatient_sms <dbl>, diagnosis_code_sms <dbl>,
## #   enroll_age_sms <dbl>, diagnosis_eng_sms <chr>, econ_any_items <dbl>,
## #   curr_commune <chr>